Following our live chat session earlier today, I am pleased to inform you the feature you are looking for with SQL Data Compare and the SQL Data Compare API will be available in the next version of SQL Data Compare.

Version 8 of SQL Data Compare will be released early next month, August 2009.

SQL Data Compare V8 is now available. The Professional Edition contains the feature to be able to compare against script folders.

The update you are seeking for the SQL Comparison SDK and the Data Compare API's is to be released later this month (August 2009). This update will include the code examples for comparing against script folders.